• BMB Reports
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• 제52권9호
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• pp.540-547
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• 2019

Immune repertoire is a collection of enormously diverse adaptive immune cells within an individual. As the repertoire shapes and represents immunological conditions, identification of clones and characterization of diversity are critical for understanding how to protect ourselves against various illness such as infectious diseases and cancers. Over the past several years, fast growing technologies for high throughput sequencing have facilitated rapid advancement of repertoire research, enabling us to observe the diversity of repertoire at an unprecedented level. Here, we focus on B cell receptor (BCR) repertoire and review approaches to B cell isolation and sequencing library construction. These experiments should be carefully designed according to BCR regions to be interrogated, such as heavy chain full length, complementarity determining regions, and isotypes. We also highlight preprocessing steps to remove sequencing and PCR errors with unique molecular index and bioinformatics techniques. Due to the nature of massive sequence variation in BCR, caution is warranted when interpreting repertoire diversity from error-prone sequencing data. Furthermore, we provide a summary of statistical frameworks and bioinformatics tools for clonal evolution and diversity. Finally, we discuss limitations of current BCR-seq technologies and future perspectives on advances in repertoire sequencing.

• IMMUNE NETWORK
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• 제3권3호
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• pp.227-234
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• 2003

Background: Immunoglobulin (Ig) light chain repertoire has been implicated as a critical determinant in regulation of autoreactive B cells and production of pathogenic anti-DNA antibodies in systemic lupus erythematosus (SLE). We analyzed the impact of Ig ${\lambda}$ chain repertoire on development of autoimmunity in patients with SLE. Methods: We obtained genomic DNA from individual peripheral CD19+ B cells of 3 untreated active SLE patients, and amplified $V{\lambda}$ rearrangements from each single cell by polymerase chain reaction. Results: A total number of 208 $V{\lambda}J{\lambda}$ rearrangements were analyzed. Analyzed sequences included 158 productive rearrangements and 50 nonproductive rearrangements. The differences in $V{\lambda}$ gene usage in the productive and nonproductive repertoire of SLE patients were found compared to the non-autoimmune individuals. $V{\lambda}$ gene, 9A was significantly overrepresented in nonproducative repertoire of SLE patients (P=0.016). In the productive repertoire, $V{\lambda}$ genes, 3L and 1E were found more often in the SLE patients (P=0.001, P=0.043). When the productive and the nonproductive repertoires were compared, 9A was found significantly less in the productive repertoire in the SLE patients (P=0.000). There were no significant differences in the $J{\lambda}$ gene usage between SLE patients and non-autoimmune individuals, but $J{\lambda}2/3$ gene was the most frequently used in SLE, whereas $J{\lambda}7$ gene was the most frequently used in the normal subjects. In the productive SLE $V{\lambda}$ repertoire, 9.4% of the total sequences employed identical CDR3. It was particularly striking to find 7 identical versions of the 1G-$J{\lambda}2/3$ $V{\lambda}J{\lambda}$ rearrangements from one patient and 3 of the same sequence from another patient. Notably, identical $V{\lambda}$ junctions in the SLE patients utilized significantly more homologous joining compared to $V{\lambda}$ junctions of the normal adults (P=0.044). Conclusion: These data demonstrate regulation of ${\lambda}$ light chain expression in the SLE patients by selection of unique $V{\lambda}$ genes. Also, biased selection and clonal expansion of particular $V{\lambda}$ rearrangements are apparent in the SLE ${\lambda}$ repertoire.

• Journal of Korean Neurosurgical Society
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• 제64권4호
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• pp.505-513
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• 2021

Objective : The adaptive immune response following subarachnoid hemorrhage (SAH) is not well understood. We evaluated and compared the T cell receptor (TCR) immune repertoire of good-grade and poor-grade SAH patients to elucidate the T cell immunology after ictus. Methods : Peripheral blood from six SAH patients was collected at two different times, admission and at the 7-day follow-up. Composition and variation of the TCR β-chain (TCRB) complimentary determining regions (CDR) 3 repertoire was examined using high-throughput sequencing; the analysis was based on sampling time and disease severity (good vs. poor-grade SAH). Results : Clonality at admission and follow-up were 0.059 (0.037-0.038) and 0.027 (0.014-0.082) (median, 25th-75th percentile). Poor-grade SAH (0.025 [0.011-0.038]) was associated with significantly lower clonality than good-grade SAH (0.095 [0.079-0.101]). Poor-grade SAH patients had higher diversity scores than good-grade SAH patients. CDR length was shorter in good-grade SAH vs. poor-grade SAH. Differences in clonotype distribution were more prominent in TCRBV gene segments than TCRBJ segments. TCRBV19-01/TCRBJ02-04 and TCRBV28-01/TCRBJ02-04 were the most increased and the most decreased V-J pairs in the 7-day follow-up compared to admission in good-grade SAH. The most increased and decreased V-J pairs in poor-grade SAH patients were TCRBV28-01/TCRBJ02-06 and TCRBV30-01/TCRBJ02-04, respectively. Conclusion : The TCRB repertoire is dynamic in nature following SAH. TCRB repertoire may facilitate our understanding of adaptive immune response according to SAH severity.

• Animal cells and systems
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• 제9권2호
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• pp.47-55
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• 2005

Avian vocalization has been main topics in studying animal communication. The structure and usage as well as development and function of vocalization vary enormously among species and even among populations, and thus we reviewed the general patterns of song learning and the consequences of song communication in birds at the behavioural level: first, we compared the different learning phenomena between non-songbird and songbird, and we investigated the learning process of songbird both in the field and in the lab, which are needed to fully understand vocal communication. Second, we discussed a recent trend of sexual selection hypothesis explaining the structural and functional diversity of song in songbirds with repertoire and presented how the repertoire is actually used between neighbours based on individual recognition.

• Animal cells and systems
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• 제13권1호
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• pp.91-96
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• 2009

The size of song repertoires mainly provides evidence for explaining sexual selection for female choice as well as male-male competition. We investigated the role of oriental great reed warbler songs (Acrocephalus orientalis) of breeding territorial males. Early arrived males possessed larger song repertoires, paired earlier, and tended to become polygynous. No correlation was found between arrival date and territory size, but polygynous males significantly occupied larger territories than non polygynous males. Song sharing was low among males and the degree of similarity did not relate with spatial distance. Our results suggest that song repertoire of the oriental great reed warbler males play a role in female choice, where territory quality may affect male pairing success.

• 한국전자거래학회지
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• 제26권4호
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• pp.133-154
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• 2021

현대인에게 가장 보편적이고 융합적인 미디어인 스마트 폰은 애플리케이션이라는 비히클을 갖는 뉴미디어이다. 이 연구는 미디어 사용자들은 어떻게 레퍼토리를 구성하여 미디어를 이용하고 있는지를 파악하고자 2019년 11월, 4주 동안의 개인별 모바일 이용행동 로그 데이터를 이용하여 모바일 애플리케이션 카테고리별 미디어 이용량을 중심으로 군집 분석을 실시하고, 최종적으로 8개의 모바일 미디어 레퍼토리 유형별 집단을 분류하였다. 8개의 각 미디어 레퍼토리 그룹은 애플리케이션 카테고리별 절대적 이용량과 타 그룹 대비 상대적 이용량에서 차이를 보였으며, 데모그라픽적 분포에서도 집단간 차이를 보였다. 이 연구는 모바일 미디어 레퍼토리를 규명해 냈다는 학문적 기여뿐만 아니라 기존의 k-means clustering에 의존적이었던 군집 분석을 SOM(Sefl-Organized Map)을 이용하여 프로토벡터를 추출하고 이 프로토벡터를 이용하여 k-means clustering을 실시하는 이단계 접근법(two-step approach)을 시도함으로써, 기존 k-means clustering이 갖고 있는 '이상치(outlier)'나 '결측치'에 민감했던 한계점을 극복하고 더 나은 성능의 분석 결과를 도출하고 있음을 보여준다는 점에서 방법론적으로도 의미를 갖는다. 또한 모바일 미디어 이용 행동의 유형 분류 연구는 전자거래 서비스를 이용하는 고객을 유형분류하고, 각 고객 유형에 맞는 고객 관리 서비스를 집행해야 하는 실무진이 고객 행동 로그 데이터를 기반으로 고객의 구조를 파악하고 각 고객 집단에 적합한 서비스 또는 마케팅 의사결정을 차별적으로 집행해야 하는 전자거래 커뮤니티에 실무적 가이드를 제공한다는 점에서도 의미를 갖고 있다.

• 한국콘텐츠학회논문지
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• 제15권2호
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• pp.196-207
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• 2015

본 연구는 '미디어-콘텐츠 레퍼토리'(미디어 이용자들이 주로 소비하는 미디어-콘텐츠 조합)를 소개하고 이에 따른 미디어 이용자들의 유형별 차이를 분석하였다. 스마트폰, 태블릿, PC, TV의 네 가지 미디어와 영화, 방송, 음악, 게임의 네 가지 콘텐츠로 미디어-콘텐츠 조합을 구성하여 각 조합 별 이용 시간에 따라 5개의 레퍼토리 군집을 도출하고 군집 별 인구통계 변수, 개인 성향, 콘텐츠 구매 행태의 차이 분석을 실시하였다. 분석 결과, 전반적으로 미디어 이용 및 콘텐츠 구매가 적은 저이용군, 50대 이상으로 주로 TV를 이용하는 스크린이용군, 20대 중심으로 대중교통 이용 시간이 많은 버라이어티군, 20,30대 중심으로 영화 및 방송을 이용하는 선택적 집중군, 30,40대 중심으로 콘텐츠 이용량이 많은 헤비유저군 등 5개 레퍼토리 군집이 서로 다른 특성을 지니고 있음이 증명되었다. 본 연구 결과는 기존 '미디어 레퍼토리'의 개념을 확장하고 레퍼토리 별 특성에 대한 심층 분석을 실시했다는 점에서 이론적 시사점을, 플랫폼 운영자와 콘텐츠 제작자들에게 각 이용자 그룹의 특성을 제공하고 세부 타깃별 전략에 대한 방향성을 제시했다는 점에서 실무적 시사점을 지닌다.

• 한국콘텐츠학회논문지
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• 제18권11호
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• pp.13-29
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• 2018

새로운 형태의 방송으로서 인터넷 개인 방송은 점차 많은 이들의 일상 생활 속에서 소비되고 있으며, 시장과 산업 측면에서 그 영향력이 확대되고 있다. 그럼에도 불구하고, 아직까지 인터넷 개인 방송과 관련된 연구는 제한적이다. 본 연구는 장르 레퍼토리 개념을 바탕으로 인터넷 개인 방송 이용자들의 장르 소비구조가 어떤 특성을 가지고 있는지 살펴보고, 이와 더불어 어떤 요인들이 이러한 이용자들의 장르 소비구조에 영향을 미치는 지를 검증하고자 하였다. 특히, 본 연구는 국내 대표적 인터넷 개인 방송 플랫폼인 <아프리카 TV> 이용자를 중심으로 이러한 요인들을 탐색하고 검증해본다. 본 연구의 결과, 연령, 감각추구성향, 정보취득 동기 및 사회적 실재감이 이용자의 인터넷 개인 방송 장르 레퍼토리에 영향을 미치는 것으로 나타났다. 더불어 사회적 실재감이 즐거움 동기와 장르 레퍼토리 사이에서 조절 효과를 보이는 것으로 나타났다.

• ALGAE
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• 제35권2호
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• pp.133-144
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• 2020

Pythium porphyrae is responsible for devastating outbreaks in seaweed farms of Pyropia, the most valuable cultivated seaweed worldwide. While the genus Pythium contains many well studied pathogens, the genome of P. porphyrae has yet to be sequenced. Here we report the first available gene repertoire of P. porphyrae and a preliminary analysis of pathogenicity-related genes. Using ab initio detection strategies, similarity based and manual annotation, we found that the P. porphyrae gene repertoire is similar to classical phytopathogenic Pythium species. This includes the absence of expanded RxLR effector family and the detection of classical pathogenicity-related genes like crinklers, glycoside hydrolases, cellulose-binding elicitor lectin-like proteins and elicitins. We additionally compared this dataset to the proteomes of 8 selected Pythium species. While 34% of the predicted proteome appeared specific to P. porphyrae, we could not attribute specific enzymes to the degradation of red algal biomass. Conversely, we detected several cellulases and a cutinase conserved with plant-pathogenic Pythium species. Together with the recent report of P. porphyrae triggering disease symptoms on several plant species in lab-controlled conditions, our findings add weight to the hypothesis that P. porphyrae is a reformed plant pathogen.

• 한국동물학회:뉴스레터
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• 제12권2호
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• pp.84.1-84
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• 1995

No Abstract, See Full Text